Merge pull request #5082 from RosettaCommons/vmullig/make_helical_bundle_predict_public Make the helical_bundle_predict app into a public app This seems stable enough to make it public, and I've had a few requests from external Rosetta users who can see the documentation for the app but who can't access the app itself. Tasks: - [x] Move `helical_bundle_predict.cc` from `apps/pilot/vmullig` to `apps/public/helical_bundle`. - [x] Update tracer output. - [x] Add CitationManager functions. - [x] Check that there are good integration tests. (I think I wrote some.) - [x] Check that integration tests produce reasonable output. - [x] Check that MPI tests produce reasonable output. - [x] Beauty. - [x] Check documentation and update accordingly.

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Merge pull request #5062 from RosettaCommons/lqtza/update-snugdock-sci-test Update SnugDock Scientific Test to Use CAPRI Metrics

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Merge pull request #5079 from RosettaCommons/vmullig/suppress_unnecessary_warning Suppress a warning message in a context in which the thing that it warns about is not an issue. This PR suppresses warnings about out-of-date residue connections in a context in which we're about to update the residue connections anyways. Users have raised questions about this unnecessary warning in the past, thinking that it indicates something going wrong when it does not. This is expected to cause cosmetic changes to a bunch of integration tests, so I'm pulling it out into its own pull request.

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Merge pull request #5075 From branch aleaverfay/hotfix_rama_ats_w_dof_derivs Fix a segfault that shows up when using cartesian minimization with the "old" (pre ref2015) rama term on termini. Now, the RamachandranEnergy class checks residues to see that they're not termini before appending the dof-deriv atoms for their phi or psi, since if they are termini, then those atoms don't exist. The Ramachandran class (which defines the potential) uses logic to decide whether a residue should have its energy counted; that logic needs to be invoked by the RamachandranEnergy class in its atoms_with_dof_derivatives function. Thanks for the heads up, Florian and Julia! Thanks for the help in zeroing in out the problem, TJ!

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Merge pull request #5070 from RosettaCommons/vmullig/remove_metal_connections_mover Add a mover that removes connections that were added by the -auto_setup_metals flag or the SetupMetalsMover It can be convenient to be able to remove bonds between metal-liganding residues and metals (_e.g._ for mutagenesis protocols in which metal-coordinating positions are mutated). This pull request aims to add a mover that does this. The mover will: - Remove the bonds between liganding residues and metals. - Remove the custom variant types from the residues. - Remove the custom variant types from the metals. - If a residue selector is provided, this behaviour will only apply when a liganding residue _and_ the metal are selected by the selector. Otherwise, it will apply to the whole pose. Tasks: - [x] Add the mover. - [x] parse_my_tag() - [x] provide_xml_schema() - [x] apply() - [x] Unit tests. - [x] For applying to whole pose. - [x] For applying to selection. - [x] Documentation. - [x] Pull request #4980 should be merged before this one. - [x] This PR should be updated with changes from PR #4980 (simplified interface for CitationManager). - [x] Beauty.

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Merge pull request #4980 from RosettaCommons/roccomoretti/cleanup_citation_manager Simplify interface for using CitationManager. There was way too much boilerplate involved with adding citation manager functions, pretty much all of which is unneeded. This PR reduces the interface for most usage down to one: a void provide_citation_info(basic::citation_manager::CitationCollectionList & citations) const member function. The current CitationCollection and the UnpublishedModuleInfo have been unified under a simple CitationCollectionBase class, which now means that both cited and uncited can be added to the same CitationCollectionList, and the CitationManager will deconvolute them when it needs to. The CitationCollectionList is basically a glorified vector1 with convenience functions to add() citation collections to it. It's set up not only to be able to add CitationCollection and UnpublishedModuleInfo (pointer) objects, but has some template magic which means that you can citations.add() sub-objects directly, which will automatically invoke their provide_citation_info() member function, making the implementation of the provide_citation_info() functions much simpler. There shouldn't be any change to what is actually printed, modulo potential order rearrangement.

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Merge pull request #5031 from RosettaCommons/roccomoretti/v3000_sdf_parser Update the V3000 SDF parser. It looks like the V3000 format SDF parser wasn't working properly. (And wasn't tested.)

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Merge pull request #5049 from RosettaCommons/roccmoretti/disable_ligand_dock_performance Disable the LigandDockProtocol performance test. This test is one of the noisiest performance test. (Probably because it's attempting to do too much in each cycle.) Additionally, it's testing an old, outdated protocol. If we want to re-enable this, we probably want to do more granular testing (different tests for each step), and test the most recent version of the protocol.

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Merge pull request #5047 from RosettaCommons/roccomoretti/database_md5_mpi Fix database_md5 MPI issue. My recent changes to the database_md5 test didn't work 100% with the MPI build, as there's some spurious lines which now get printed (and diffed) there. Move the log files which we don't need to compare to a .ignore file instead.

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Merge pull request #4991 from RosettaCommons/francesc45/logic_residue_selector Add LogicResidueSelector which takes booleans in its option

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Merge pull request #5069 from RosettaCommons/JackMaguire/FixJD3Issue Fixing and commenting JD3NodeManagersTests:test_stop_early unit test

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Merge pull request #5068 from RosettaCommons/sergey/binder fixing PyRosetta notebook tests

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Merge pull request #5067 from RosettaCommons/sergey/binder updating PyRosetta memory requirements during building

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Merge pull request #5064 from RosettaCommons/roccomoretti/fix_clang_tidy Fix Clang tidy issue with ResidueTypeSet. Sergey's recent changes caused clang-tidy to point out issues with ResidueTypeSet. Resolve these.

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Merge pull request #5032 from RosettaCommons/roccomoretti/license Add a LICENSE.md Include the current Academic license with the code. Be sure to point out that this is the Academic version, and doesn't apply to commercial users. There's some potential deficiencies in the current text, but those would need to get fixed upstream at UW first.

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Merge pull request #5063 from RosettaCommons/roccomoretti/fix_thread_frag_picker Attempt to stabilize integration.thread fragment_picker test. The fragment_picker test in the multithreaded case is noisy on the test server. This looks to be due to fragment sorting. Depending on when the threads finish, equivalently scored fragments can come in different orders. Attempt to stabilize this by sorting on FragID when the scores are identical.

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